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Klećkowska-Nawrot JE, Goździewska-Harłajczuk K, Barszcz K, Stegmann KO. Morphological examination of the visual system and orbital region in the red panda (Ailurus fulgens fulgens). BMC Vet Res 2024; 20:284. [PMID: 38956555 PMCID: PMC11221124 DOI: 10.1186/s12917-024-04152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
OBJECTIVES The red panda is currently the only surviving member of the Ailuridae family in the Caniformia suborder. In this study, we provide data on anatomical, morphometric, histological and histochemical examination of the orbital region, eyelids, orbital gland, and eye tunics in two adult males Ailurus fulgens fulgens from the Wroclaw Zoological Garden, Poland. METHODS The study involved morphometric analysis of the eyeball and selected accessory organs of the eye, along with analysis of the bony orbit, including its morphometry, macroscopic, and microscopic evaluation. Microscopic evaluation encompassed histological and histochemical staining, with the former involving hematoxylin & eosin (H&E), Movat pentachrome, picro-Mallory trichrome, Fontana-Masson, and the latter including PAS, AB pH 1.0, AB pH 2.5; AB pH 2.5/PAS, and HDI. RESULTS The upper (UE) and lower (LE) eyelids presented well-developed tarsal glands, sebaceous glands, and a characteristic simple alveolar gland (producing a mucous secretion). The palpebral part of the lacrimal gland was present. A single lymphoid follicle was observed only in the upper eyelids. The superficial gland of the third eyelid (SGTE) was a multilobar acinar complex that produces mucous secretion and is contained within the interlobular ducts of numerous aggregates of lymph nodes. The third eyelid (TE) was T-shaped and composed of hyaline tissue, containing CALT. The lacrimal gland (LG) also revealed a multilobar acinar complex that produced mucous secretion, with a single lymphoid follicle. The cornea consisted of 4 layers, as Bowman's membrane was absent. The Vogt palisades composed of 7-10 layers of epithelial cells were demonstrated. The pupil was horizontally ovoid at rest (post-mortem). The sphincter pupil and the dilator pupil were well developed. Macroscopically, the tapetum lucidum appeared as a milky, non-opalescent crescent. Histologically, the choroidal tapetum lucidum cellulosum consisted of 5 to 9 layers of loosely packed oval cells. The retina showed a composition similar to that of terrestrial nocturnal carnivores. CONCLUSIONS The results of our research indicate that the anatomical features of the eye and orbital region in the red panda share similarities with those described in the Musteloidea clade, as well as the Canidae and Ursidae families.
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Affiliation(s)
- Joanna E Klećkowska-Nawrot
- Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Kozuchowska 1, Wroclaw, 51-631, Poland
| | - Karolina Goździewska-Harłajczuk
- Department of Biostructure and Animal Physiology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Kozuchowska 1, Wroclaw, 51-631, Poland.
| | - Karolina Barszcz
- Department of Morphological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-787, Poland.
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2
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Park T, Burin G, Lazo-Cancino D, Rees JPG, Rule JP, Slater GJ, Cooper N. Charting the course of pinniped evolution: insights from molecular phylogeny and fossil record integration. Evolution 2024; 78:1212-1226. [PMID: 38644688 DOI: 10.1093/evolut/qpae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 04/23/2024]
Abstract
Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these 2 rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses, however, experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12 to 6 Ma, possibly due to changing sea levels and/or competition with otariids (eared seals). Historical biogeographic analyses, including fossil data, allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.
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Affiliation(s)
- Travis Park
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
- Sciences, Museums Victoria, Melbourne, Australia
| | - Gustavo Burin
- Science Group, Natural History Museum London, London, United Kingdom
| | - Daniela Lazo-Cancino
- Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Joseph P G Rees
- Science Group, Natural History Museum London, London, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James P Rule
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Natalie Cooper
- Science Group, Natural History Museum London, London, United Kingdom
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3
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Sosale MS, Roelke-Parker M, Machange GA, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome of Meller's mongoose ( Rhynchogale melleri). Mitochondrial DNA B Resour 2024; 9:432-436. [PMID: 38586507 PMCID: PMC10993741 DOI: 10.1080/23802359.2024.2333567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Meller's mongoose (Rhynchogale melleri) is a member of the family Herpestidae (Mammalia: Carnivora) and the sole species in the genus Rhynchogale. It is primarily found in savannas and open woodlands of eastern sub-Saharan Africa. Here, we report the first complete mitochondrial genome for a female Meller's mongoose collected in Tanzania, generated using a genome-skimming approach. The mitogenome had a final length of 16,644 bp and a total of 37 annotated genes. Phylogenetic analysis validated the placement of this species in the herpestid subfamily Herpestinae. Ultimately, the outcomes of this research offer a genetic foundation for future studies of Meller's mongoose.
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Affiliation(s)
- Medhini S. Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Melody Roelke-Parker
- Laboratory Animal Science Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Henrique V. Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, Virginia, USA
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4
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Mitchell DR, Sherratt E, Weisbecker V. Facing the facts: adaptive trade-offs along body size ranges determine mammalian craniofacial scaling. Biol Rev Camb Philos Soc 2024; 99:496-524. [PMID: 38029779 DOI: 10.1111/brv.13032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023]
Abstract
The mammalian cranium (skull without lower jaw) is representative of mammalian diversity and is thus of particular interest to mammalian biologists across disciplines. One widely retrieved pattern accompanying mammalian cranial diversification is referred to as 'craniofacial evolutionary allometry' (CREA). This posits that adults of larger species, in a group of closely related mammals, tend to have relatively longer faces and smaller braincases. However, no process has been officially suggested to explain this pattern, there are many apparent exceptions, and its predictions potentially conflict with well-established biomechanical principles. Understanding the mechanisms behind CREA and causes for deviations from the pattern therefore has tremendous potential to explain allometry and diversification of the mammalian cranium. Here, we propose an amended framework to characterise the CREA pattern more clearly, in that 'longer faces' can arise through several kinds of evolutionary change, including elongation of the rostrum, retraction of the jaw muscles, or a more narrow or shallow skull, which all result in a generalised gracilisation of the facial skeleton with increased size. We define a standardised workflow to test for the presence of the pattern, using allometric shape predictions derived from geometric morphometrics analysis, and apply this to 22 mammalian families including marsupials, rabbits, rodents, bats, carnivores, antelopes, and whales. Our results show that increasing facial gracility with size is common, but not necessarily as ubiquitous as previously suggested. To address the mechanistic basis for this variation, we then review cranial adaptations for harder biting. These dictate that a more gracile cranium in larger species must represent a structural sacrifice in the ability to produce or withstand harder bites, relative to size. This leads us to propose that facial gracilisation in larger species is often a product of bite force allometry and phylogenetic niche conservatism, where more closely related species tend to exhibit more similar feeding ecology and biting behaviours and, therefore, absolute (size-independent) bite force requirements. Since larger species can produce the same absolute bite forces as smaller species with less effort, we propose that relaxed bite force demands can permit facial gracility in response to bone optimisation and alternative selection pressures. Thus, mammalian facial scaling represents an adaptive by-product of the shifting importance of selective pressures occurring with increased size. A reverse pattern of facial 'shortening' can accordingly also be found, and is retrieved in several cases here, where larger species incorporate novel feeding behaviours involving greater bite forces. We discuss multiple exceptions to a bite force-mediated influence on facial proportions across mammals which lead us to argue that ecomorphological specialisation of the cranium is likely to be the primary driver of facial scaling patterns, with some developmental constraints as possible secondary factors. A potential for larger species to have a wider range of cranial functions when less constrained by bite force demands might also explain why selection for larger sizes seems to be prevalent in some mammalian clades. The interplay between adaptation and constraint across size ranges thus presents an interesting consideration for a mechanistically grounded investigation of mammalian cranial allometry.
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Affiliation(s)
- D Rex Mitchell
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia, 5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, 2522, Australia
| | - Emma Sherratt
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- South Australian Museum, Adelaide, South Australia, 5000, Australia
| | - Vera Weisbecker
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia, 5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, New South Wales, 2522, Australia
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Belyaev RI, Nikolskaia P, Bushuev AV, Panyutina AA, Kozhanova DA, Prilepskaya NE. Running, jumping, hunting, and scavenging: Functional analysis of vertebral mobility and backbone properties in carnivorans. J Anat 2024; 244:205-231. [PMID: 37837214 PMCID: PMC10780164 DOI: 10.1111/joa.13955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 10/15/2023] Open
Abstract
Carnivorans are well-known for their exceptional backbone mobility, which enables them to excel in fast running and long jumping, leading to them being among the most successful predators amongst terrestrial mammals. This study presents the first large-scale analysis of mobility throughout the presacral region of the vertebral column in carnivorans. The study covers representatives of 6 families, 24 genera and 34 species. We utilized a previously developed osteometry-based method to calculate available range of motion, quantifying all three directions of intervertebral mobility: sagittal bending (SB), lateral bending (LB), and axial rotation (AR). We observed a strong phylogenetic signal in the structural basis of the vertebral column (vertebral and joint formulae, length proportions of the backbone modules) and an insignificant phylogenetic signal in most characteristics of intervertebral mobility. This indicates that within the existing structure (stabilization of which occurred rather early in different phylogenetic lineages), intervertebral mobility in carnivorans is quite flexible. Our findings reveal that hyenas and canids, which use their jaws to seize prey, are characterized by a noticeably elongated cervical region and significantly higher SB and LB mobility of the cervical joints compared to other carnivorans. In representatives of other carnivoran families, the cervical region is very short, but the flexibility of the neck (both SB and LB) is significantly higher than that of short-necked odd-toed and even-toed ungulates. The lumbar region of the backbone in carnivorans is dorsomobile in the sagittal plane, being on average ~23° more mobile than in artiodactyls and ~38° more mobile than in perissodactyls. However, despite the general dorsomobility, only some representatives of Canidae, Felidae, and Viverridae are superior in lumbar flexibility to the most dorsomobile ungulates. The most dorsomobile artiodactyls are equal or even superior to carnivorans in their ability to engage in dorsal extension during galloping. In contrast, carnivorans are far superior to ungulates in their ability to engage ventral flexion. The cumulative SB in the lumbar region in carnivorans largely depends on the mode of running and hunting. Thus, adaptation to prolonged and enduring pursuit of prey in hyenas is accompanied by markedly reduced SB flexibility in the lumbar region. A more dorsostable run is also a characteristic of the Ursidae, and the peculiar maned wolf. Representatives of Felidae and Canidae have significantly more available SB mobility in the lumbar region. However, they fully engage it only occasionally at key moments of the hunt associated with the direct capture of the prey or when running in a straight line at maximum speed.
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Affiliation(s)
- Ruslan I. Belyaev
- A.N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesMoscowRussian Federation
| | - Polina Nikolskaia
- Geological InstituteRussian Academy of SciencesMoscowRussian Federation
| | - Andrey V. Bushuev
- Department of Vertebrate Zoology, Faculty of BiologyLomonosov Moscow State UniversityMoscowRussian Federation
| | | | - Darya A. Kozhanova
- Department of Paleontology, Faculty of GeologyLomonosov Moscow State UniversityMoscowRussian Federation
| | - Natalya E. Prilepskaya
- A.N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesMoscowRussian Federation
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Osozawa S. Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans. Ecol Evol 2023; 13:e10827. [PMID: 38116126 PMCID: PMC10728886 DOI: 10.1002/ece3.10827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1-106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K-Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non-avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial-interglacial cycles, thereby causing significant climatic changes.
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Affiliation(s)
- Soichi Osozawa
- Faculty of Science, Institute of Geology and PaleontologyTohoku UniversitySendaiJapan
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7
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Mora JM, Ruedas LA. Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes. Zootaxa 2023; 5357:451-501. [PMID: 38220635 DOI: 10.11646/zootaxa.5357.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Indexed: 01/16/2024]
Abstract
Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.
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Affiliation(s)
- Jos Manuel Mora
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA; Carrera de Gestin Ecoturstica; Sede Central; Universidad Tcnica Nacional; Alajuela; Costa Rica.
| | - Luis A Ruedas
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA.
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8
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Kliver S, Houck ML, Perelman PL, Totikov A, Tomarovsky A, Dudchenko O, Omer AD, Colaric Z, Weisz D, Aiden EL, Chan S, Hastie A, Komissarov A, Ryder OA, Graphodatsky A, Johnson WE, Maldonado JE, Pukazhenthi BS, Marinari PE, Wildt DE, Koepfli KP. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). J Hered 2023; 114:539-548. [PMID: 37249392 PMCID: PMC10848218 DOI: 10.1093/jhered/esad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/27/2023] [Indexed: 05/31/2023] Open
Abstract
The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.
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Affiliation(s)
- Sergei Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, Copenhagen, Denmark
| | - Marlys L Houck
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Polina L Perelman
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Azamat Totikov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Andrey Tomarovsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, United States
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Saki Chan
- Department of Research and Development, Bionano Genomics, San Diego, CA, United States
| | - Alex Hastie
- Department of Research and Development, Bionano Genomics, San Diego, CA, United States
| | - Aleksey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, Russia
| | - Oliver A Ryder
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Alexander Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Warren E Johnson
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Loyola University Maryland, Baltimore, MD, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Paul E Marinari
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - David E Wildt
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, United States
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9
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Austin RM, Eriksen PM, Bachmann L. Complete mitochondrial genome of the Galápagos sea lion, Zalophuswollebaeki (Carnivora, Otariidae): paratype specimen confirms separate species status. Zookeys 2023; 1166:307-313. [PMID: 38328668 PMCID: PMC10848830 DOI: 10.3897/zookeys.1166.103247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/04/2023] [Indexed: 02/09/2024] Open
Abstract
The endangered Galápagos sea lion (Zalophuswollebaeki) inhabits the Galápagos Islands off the coast of Ecuador. We present a complete mitochondrial genome (16 465 bp) of a female paratype from the collections of the Natural History Museum Oslo, Norway, assembled from next-generation sequencing reads. It contains all canonical protein-coding, rRNA, tRNA genes, and the D-loop region. Sequence similarity is 99.93% to a previously published conspecific mitogenome sequence and 99.37% to the mitogenome sequence of the sister species Z.californianus. Sequence similarity of the D-loop region of the Z.wollebaeki paratype mitogenome is >99%, while the sequence difference to the Z.californianus sequences exceeds 2.5%. The paratype mitogenome sequence supports the taxonomic status of Z.wollebaeki as a separate species.
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Affiliation(s)
- Rita M. Austin
- Frontiers in Evolutionary Zoology, Natural History Museum of Oslo, University of Oslo, Oslo, NorwayUniversity of OsloOsloNorway
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USANational Museum of Natural History, Smithsonian InstitutionWashington D.C.United States of America
| | - Pia Merete Eriksen
- Frontiers in Evolutionary Zoology, Natural History Museum of Oslo, University of Oslo, Oslo, NorwayUniversity of OsloOsloNorway
| | - Lutz Bachmann
- Frontiers in Evolutionary Zoology, Natural History Museum of Oslo, University of Oslo, Oslo, NorwayUniversity of OsloOsloNorway
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10
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Liu Y, Pu Y, Chen S, Wang X, Murphy RW, Wang X, Liao R, Tang K, Yue B, Liu S. Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology. Ecol Evol 2023; 13:e9944. [PMID: 37082328 PMCID: PMC10111237 DOI: 10.1002/ece3.9944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.
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Affiliation(s)
- Yingxun Liu
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Yingting Pu
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Shunde Chen
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Xuming Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | | | - Xin Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | - Rui Liao
- Sichuan Academy of ForestryChengduSichuanChina
| | - Keyi Tang
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Bisong Yue
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Shaoying Liu
- Sichuan Academy of ForestryChengduSichuanChina
- Ecological Restoration and Conservation for Forest and Wetland Key Laboratory of Sichuan ProvinceSichuan Academy of ForestryChengduSichuanChina
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11
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Sosale MS, Songsasen N, İbiş O, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica). Gene 2023; 866:147303. [PMID: 36854348 DOI: 10.1016/j.gene.2023.147303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/27/2023]
Abstract
The golden jackal (Canis aureus) is a canid species found across southern Eurasia. Several subspecies of this animal have been genetically studied in regions such as Europe, the Middle East, and India. However, one subspecies that lacks current research is the Indochinese jackal (Canis aureus cruesemanni), which is primarily found in Southeast Asia. Using a genome skimming approach, we assembled the first complete mitochondrial genome for an Indochinese jackal from Thailand. To expand the number of available Canis aureus mitogenomes, we also assembled and sequenced the first complete mitochondrial genome of a golden jackal from Turkey, representing the C. a. moreotica subspecies. The mitogenomes contained 37 annotated genes and are 16,729 bps (C. a. cruesemanni) and 16,669 bps (C. a. moreotica) in length. Phylogenetic analysis with 26 additional canid mitogenomes and analyses of a cytochrome b gene-only data set together support the Indochinese jackal as a distinct and early-branching lineage among golden jackals, thereby supporting its recognition as a possible subspecies. These analyses also demonstrate that the golden jackal from Turkey is likely not a distinct lineage due to close genetic relationships with golden jackals from India and Israel.
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Affiliation(s)
- Medhini S Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA.
| | - Nucharin Songsasen
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA
| | - Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey; Vectors and Vector-Borne Diseases Implementation and Research Center, Erciyes University, Kayseri, Turkey
| | - Cody W Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA; Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA.
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12
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Genetic relationships among populations of the small Indian mongoose (Urva auropunctata) introduced in Japan. MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
The small Indian mongoose, Urva auropunctata, is one of the most notorious invasive species in the world. In Japan, the mongoose was introduced to Amami, Kyushu (Kiire region), and Okinawa Islands. Currently, an eradication program for the Amami population is proving successful. To prevent reinvasion and conserve biodiversity, it would be advantageous to investigate the origin and dispersal history of introduced mongoose populations in Japan. We determined the mitochondrial genome of a mongoose from the Okinawa population and confirmed that the systematic status of the mongoose is Urva auropunctata. We also found two haplotypes of cytochrome b in the Amami population, one of which is common among the Okinawa, Amami, and Kiire populations. Based on our microsatellite analysis, the three populations were genetically different from each other. Furthermore, with a low pairwise FST value, the Kiire population was closer to the Okinawa than the Amami population. Our results suggest that the Okinawa population could be the source of the Amami and Kiire populations. These results align with historical records of mongoose in Japan and clarify its genetic status. Our results should aid the prediction of the pathway through which a new invasion will likely occur.
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13
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Winter S, Fennessy J, Janke A, Nilsson MA. Northern olingo (Bassaricyon gabbi), zorilla (Ictonyx striatus), and honey badger (Mellivora capensis) mitochondrial genomes and a phylogeny of Musteloidea. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1089641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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14
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The current state of carnivore cognition. Anim Cogn 2023; 26:37-58. [PMID: 36333496 DOI: 10.1007/s10071-022-01709-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
The field of animal cognition has advanced rapidly in the last 25 years. Through careful and creative studies of animals in captivity and in the wild, we have gained critical insights into the evolution of intelligence, the cognitive capacities of a diverse array of taxa, and the importance of ecological and social environments, as well as individual variation, in the expression of cognitive abilities. The field of animal cognition, however, is still being influenced by some historical tendencies. For example, primates and birds are still the majority of study species in the field of animal cognition. Studies of diverse taxa improve the generalizability of our results, are critical for testing evolutionary hypotheses, and open new paths for understanding cognition in species with vastly different morphologies. In this paper, we review the current state of knowledge of cognition in mammalian carnivores. We discuss the advantages of studying cognition in Carnivorans and the immense progress that has been made across many cognitive domains in both lab and field studies of carnivores. We also discuss the current constraints that are associated with studying carnivores. Finally, we explore new directions for future research in studies of carnivore cognition.
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15
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Gray A, Brito JC, Edwards CW, Figueiró HV, Koepfli KP. First complete mitochondrial genome of the Saharan striped polecat ( Ictonyx libycus). MITOCHONDRIAL DNA PART B 2022; 7:1957-1960. [DOI: 10.1080/23802359.2022.2141080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Autumn Gray
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
| | - José C. Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Henrique V. Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Fairfax, VA, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Virginia, USA
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16
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Duplication, Loss, and Evolutionary Features of Specific UDP-Glucuronosyltransferase Genes in Carnivora (Mammalia, Laurasiatheria). Animals (Basel) 2022; 12:ani12212954. [DOI: 10.3390/ani12212954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
UDP-glucuronosyltransferases (UGTs) are one of the most important enzymes for xenobiotic metabolism or detoxification. Through duplication and loss of genes, mammals evolved the species-specific variety of UGT isoforms. Among mammals, Carnivora is one of the orders that includes various carnivorous species, yet there is huge variation of food habitat. Recently, lower activity of UGT1A and 2B were shown in Felidae and pinnipeds, suggesting evolutional loss of these isoforms. However, comprehensive analysis for genetic or evolutional features are still missing. This study was conducted to reveal evolutional history of UGTs in Carnivoran species. We found specific gene expansion of UGT1As in Canidae, brown bear and black bear. We also found similar genetic duplication in UGT2Bs in Canidae, and some Mustelidae and Ursidae. In addition, we discovered contraction or complete loss of UGT1A7–12 in phocids, some otariids, felids, and some Mustelids. These studies indicate that even closely related species have completely different evolution of UGTs and further imply the difficulty of extrapolation of the pharmacokinetics and toxicokinetic result of experimental animals into wildlife carnivorans.
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17
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Specific Gene Duplication and Loss of Cytochrome P450 in Families 1-3 in Carnivora (Mammalia, Laurasiatheria). Animals (Basel) 2022; 12:ani12202821. [PMID: 36290207 PMCID: PMC9597770 DOI: 10.3390/ani12202821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary In this study we investigated the specific duplication and loss events of cytochrome P450 (CYP) genes in families 1-3 in Carnivora. These genes have been recognized as essential detoxification enzymes, and, using genomic data, we demonstrated a synteny analysis of the CYP coding cluster and a phylogenetic analysis of these genes. We discovered the CYP2Cs and CYP3As expansion in omnivorous species such as the badger, the brown bear, the black bear, and the dog. Furthermore, phylogenetic analysis revealed the evolution of CYP2Cs and 3As in Carnivora. These findings are essential for the appropriate estimation of pharmacokinetics or toxicokinetic in wild carnivorans. Abstract Cytochrome P450s are among the most important xenobiotic metabolism enzymes that catalyze the metabolism of a wide range of chemicals. Through duplication and loss events, CYPs have created their original feature of detoxification in each mammal. We performed a comprehensive genomic analysis to reveal the evolutionary features of the main xenobiotic metabolizing family: the CYP1-3 families in Carnivora. We found specific gene expansion of CYP2Cs and CYP3As in omnivorous animals, such as the brown bear, the black bear, the dog, and the badger, revealing their daily phytochemical intake as providing the causes of their evolutionary adaptation. Further phylogenetic analysis of CYP2Cs revealed Carnivora CYP2Cs were divided into CYP2C21, 2C41, and 2C23 orthologs. Additionally, CYP3As phylogeny also revealed the 3As’ evolution was completely different to that of the Caniformia and Feliformia taxa. These studies provide us with fundamental genetic and evolutionary information on CYPs in Carnivora, which is essential for the appropriate interpretation and extrapolation of pharmacokinetics or toxicokinetic data from experimental mammals to wild Carnivora.
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18
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Veron G, Daniel C, Pagani P, Do Linh San E, Kitchener AC, Hassanin A. A tale of two African mongooses (Carnivora: Herpestidae): differing genetic diversity and geographical structure across a continent. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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19
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Simpson J, Kozak CA, Boso G. Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. PLoS Genet 2022; 18:e1010458. [PMID: 36240227 PMCID: PMC9604959 DOI: 10.1371/journal.pgen.1010458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/26/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Endogenous retroviruses (ERVs) found in vertebrate genomes are remnants of retroviral invasions of their ancestral species. ERVs thus represent molecular fossil records of ancient retroviruses and provide a unique opportunity to study viral-host interactions, including cross-species transmissions, in deep time. While most ERVs contain the mutated remains of the original retrovirus, on rare occasions evolutionary selection pressures lead to the co-option/exaptation of ERV genes for a host function. Here, we report the identification of two ancient related non-orthologous ERV env genes, ARTenvV and CARenvV, that are preserved with large open reading frames (ORFs) in the mammalian orders Artiodactyla and Carnivora, respectively, but are not found in other mammals. These Env proteins lack a transmembrane motif, but phylogenetic analyses show strong sequence preservation and positive selection of the env surface ORF in their respective orders, and transcriptomic analyses show a broad tissue expression pattern for both ARTenvV and CARenvV, suggesting that these genes may be exapted for a host function. Multiple lines of evidence indicate that ARTenvV and CARenvV were derived from an ancient ancestral exogenous gamma-like retrovirus that was independently endogenized in two mammalian orders more than 60 million years ago, which roughly coincides with the K-Pg mass extinction event and subsequent mammalian diversification. Thus, these findings identify the oldest known retroviral cross-ordinal transmission of a gamma-like retrovirus with no known extant infectious counterpart in mammals, and the first discovery of the convergent co-option of an ERV gene derived from the same ancestral retrovirus in two different mammalian orders.
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Affiliation(s)
- J’Zaria Simpson
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
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20
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Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Mol Ecol 2022; 31:3888-3902. [PMID: 35638312 PMCID: PMC9546496 DOI: 10.1111/mec.16554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
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Affiliation(s)
- Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil.,Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Belgium
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Lukas F K Kuderna
- Ilumina Inc., Hayward, CA, USA.,Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Nicole S Torosin
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology and Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Barcelona, Spain
| | - Ian B Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Mariluce Messias
- Department of Biology, Universidade Federal de Rondônia, Porto Velho, Brazil
| | - Maria N F da Silva
- Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
| | | | - Izeni P Farias
- Laboratory of Evolution and Animal Genetics, Universidade Federal do Amazonas, Brazil
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Brazil
| | - Fabiano R de Melo
- Department of Forestry Engineering, Universidade Federal de Viçosa, Brazil
| | - João Valsecchi
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil
| | - Tomas Hrbek
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom.,Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
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21
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Plasil M, Futas J, Jelinek A, Burger PA, Horin P. Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids. Front Genet 2022; 13:829891. [PMID: 35309138 PMCID: PMC8924298 DOI: 10.3389/fgene.2022.829891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/15/2022] [Indexed: 12/25/2022] Open
Abstract
This review summarizes the current knowledge on the major histocompatibility complex (MHC) of the family Felidae. This family comprises an important domestic species, the cat, as well as a variety of free-living felids, including several endangered species. As such, the Felidae have the potential to be an informative model for studying different aspects of the biological functions of MHC genes, such as their role in disease mechanisms and adaptation to different environments, as well as the importance of genetic diversity for conservation issues in free-ranging or captive populations. Despite this potential, the current knowledge on the MHC in the family as a whole is fragmentary and based mostly on studies of the domestic cat and selected species of big cats. The overall structure of the domestic cat MHC is similar to other mammalian MHCs following the general scheme “centromere-MHC class I-MHC class III-MHC class II” with some differences in the gene contents. An unambiguously defined orthologue of the non-classical class I HLA-E gene has not been identified so far and the class II DQ and DP genes are missing or pseudogenized, respectively. A comparison with available genomes of other felids showed a generally high level of structural and sequence conservation of the MHC region. Very little and fragmentary information on in vitro and/or in vivo biological functions of felid MHC genes is available. So far, no association studies have indicated effects of MHC genetic diversity on a particular disease. No information is available on the role of MHC class I molecules in interactions with Natural Killer (NK) cell receptors or on the putative evolutionary interactions (co-evolution) of the underlying genes. A comparison of complex genomic regions encoding NK cell receptors (the Leukocyte Receptor Complex, LRC and the Natural Killer Cell Complex, NKC) in the available felid genomes showed a higher variability in the NKC compared to the LRC and the MHC regions. Studies of the genetic diversity of domestic cat populations and/or specific breeds have focused mainly on DRB genes. Not surprisingly, higher levels of MHC diversity were observed in stray cats compared to pure breeds, as evaluated by DRB sequencing as well as by MHC-linked microsatellite typing. Immunogenetic analysis in wild felids has only been performed on MHC class I and II loci in tigers, Namibian leopards and cheetahs. This information is important as part of current conservation tasks to assess the adaptive potential of endangered wild species at the human-wildlife interface, which will be essential for preserving biodiversity in a functional ecosystem.
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Affiliation(s)
- Martin Plasil
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jan Futas
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - April Jelinek
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, VIA, Vienna, Austria
| | - Petr Horin
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
- *Correspondence: Petr Horin,
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22
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Hudson R, Szenczi P, Bánszegi O. Parental Behavior in Carnivores. ADVANCES IN NEUROBIOLOGY 2022; 27:55-78. [PMID: 36169812 DOI: 10.1007/978-3-030-97762-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The mammalian order Carnivora is generally defined as species that feed exclusively or to some degree by eating other animals. The Carnivora comprise around 280 species, divided into 16 families, 13 of which are terrestrial and 3 aquatic. Carnivores are spread across the entire planet, including the two polar regions and on land and sea. Consistent with such diverse ecologies, there is no typical pattern of parental care distinguishing carnivores from other mammals. Using examples from different taxonomic families, our aim is to illustrate the diversity of parental care in Carnivora. Major topics include parental care before and after birth of the young, paternal, and alloparental care and the process of weaning. Given the position of many carnivores at the apex of food chains, a greater understanding of their patterns of parental care as a vital part of reproductive biology is essential to conservation programs.
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Affiliation(s)
- Robyn Hudson
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| | - Péter Szenczi
- CONACyT - Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Mexico City, Mexico
| | - Oxána Bánszegi
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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23
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Abramson NI, Bodrov SY, Bondareva OV, Genelt-Yanovskiy EA, Petrova TV. A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications. PLoS One 2021; 16:e0248198. [PMID: 34797834 PMCID: PMC8604340 DOI: 10.1371/journal.pone.0248198] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023] Open
Abstract
Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.
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Affiliation(s)
- Natalia I. Abramson
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Semyon Yu. Bodrov
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Olga V. Bondareva
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Evgeny A. Genelt-Yanovskiy
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Tatyana V. Petrova
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
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24
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Meloro C, Tamagnini D. Macroevolutionary ecomorphology of the Carnivora skull: adaptations and constraints in the extant species. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The mammalian order Carnivora is characterized by a broad taxonomic and ecological diversity. By using a large sample of extant species, we tested the impact of ecological factors on carnivoran skull (cranium and mandible) morphology, taking advantage of a combined geometric morphometrics and comparative method approach. We implemented several evolutionary models to account for different tempo and mode of evolution in size and shape data. These models validated the association between skull morphology and diet at the interspecific scale. The functional distinction between pinniped (aquatic) and fissiped (mostly terrestrial) taxa was found valid only in mandible shape and cranial size. High levels of morphological disparity and evolutionary rates were identified in specialized dietary groups, and positive association between rates and disparity was found for skull size. Cranium and mandible showed consistent patterns of covariation that reflect constrained functional processes, which stabilize the ecomorphological evolution of Carnivora. Aquatic adaptations allowed carnivorans to invade and persist within novel regions of the mandibular morphospace. This ecological shift did not increase morphological disparity but occurred at a faster rate than in terrestrial species. Those species exhibit a stronger level of cranio-mandibular covariation due to constraints imposed by more demanding masticatory adaptations.
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Affiliation(s)
- Carlo Meloro
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Davide Tamagnini
- Department of Biology and Biotechnologies ‘Charles Darwin’, University of Rome La Sapienza, Rome, Italy
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Szatmári L, Cserkész T, Laczkó L, Lanszki J, Pertoldi C, Abramov AV, Elmeros M, Ottlecz B, Hegyeli Z, Sramkó G. A comparison of microsatellites and genome-wide SNPs for the detection of admixture brings the first molecular evidence for hybridization between Mustela eversmanii and M. putorius (Mustelidae, Carnivora). Evol Appl 2021; 14:2286-2304. [PMID: 34603499 PMCID: PMC8477604 DOI: 10.1111/eva.13291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022] Open
Abstract
Introgressive hybridization can pose a serious threat to endangered species which have an overlapping distribution such as in the case of two polecat species, Mustela eversmanii and M. putorius, in Europe. The population size of steppe polecat is known to continuously shrink, whereas its sister species, the European polecat, is still somehow widespread. In this study, we perform an analysis using microsatellite (SSR) and genomic (SNP) data sets to identify natural hybrids between polecats. Four populations were genotyped for eight polymorphic SSR loci, and thousands of unlinked SNPs were generated using a reduced-representation sequencing approach, RADseq, to characterize the genetic make-up of allopatric populations and to identify hybrids in the sympatric area. We applied standard population genetic analyses to characterize the populations based on their SSR allelic frequency. Only a single sample out of 48 sympatric samples showed exact intermediacy that we identified as an F1 hybrid. Additionally, one specimen was indicated in the genomic data sets as backcrossed. Other backcrosses, indicated by SSRs, were not validated by SNPs, which highlights the higher efficacy of the genomic method to identify backcrossed individuals. The low frequency of hybridization suggests that the difference in habitat preference of the two species may act as a barrier to admixture. Therefore, it is apparently unlikely that polecat populations are threatened by significant introgression. The two species showed a clear genetic differentiation using both techniques. We found higher genetic diversity values in the sympatric steppe polecat population than in the other studies on polecat populations. Although M. putorius is a hunted species in most countries, genetic diversity values indicate worse conditions in Europe than in the protected sibling species M. eversmanii. Suspending hunting and providing protected status of the former seems to be reasonable and timely.
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Affiliation(s)
- Lajos Szatmári
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - Tamás Cserkész
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
- Bükk Mammalogical Society Eger Hungary
| | - Levente Laczkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - József Lanszki
- Carnivore Ecology Research Group Szent István University, Kaposvár Campus Kaposvár Hungary
| | - Cino Pertoldi
- Department of Chemistry and Bioscience Aalborg University Aalborg Øst Denmark
- Aalborg Zoo Aalborg Denmark
| | - Alexei V Abramov
- Zoological Institute Russian Academy of Sciences Saint Petersburg Russia
| | - Morten Elmeros
- Department of Bioscience - Wildlife Ecology Aarhus University Rønde Denmark
| | | | - Zsolt Hegyeli
- Milvus Group Bird and Nature Protection Association Tîrgu Mureș Romania
| | - Gábor Sramkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
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Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Lécu A, Goodman SM, Haider J, Thanh Nguyen T. Correction: Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS One 2021; 16:e0249387. [PMID: 33780516 PMCID: PMC8007015 DOI: 10.1371/journal.pone.0249387] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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